"Manchester United is a Mancunian institution. It's a privilege to have them on our doorstep and to cover them minutely. But we are not on the club's payroll," editor Sarah Lester wrote.
"Our job is to report what's happening in the organisations that matter to our readers. And that includes our great football clubs.
"We do not publish anything lightly and all of our stories are sourced and checked. We have a responsibility to the readers who place such trust in us to faithfully report what we know and what we see."
The letter added: "It's at press conferences where our journalists get the chance to ask questions on behalf of all these supporters. To be shut out for reporting a story we know to be accurate is wrong.
"That said, we largely have a productive relationship with Manchester United and we want that to continue. Our role is that of a concerned friend. Our preference is to move on. We suggest United looks closer to home for the sources of the disquiet - rather than shooting the messenger."